Capital ship order cannot be maintained when the Discord battleship is added to a fleet -  I cant tab through the capital ships in a fleet before selecting through frigates. The Discord is always first and as you continue to tab it goes through capitals and sometimes frigates before you scroll through all the capital ships. In Diplomacy I am pretty sure that if the cap ship I wanted was listed third in the fleet on the the left pane, it took 2 tabs to get to it.

On a more whimsical note:

AI devotes too much time for titans to combat fighter screens of a system instead of attacking defense structures.
never mind, saw that was in the fixed internal list

While I think the flares around the sun are neat, much slower (and by that I mean glacial) movement would give a much better sense of size and massiveness.

O poo, there is no dedicate orifice for planet bombardment missles on the Discord. O well, maybe the missles just melt through the forward face of the ship.

For Advent, I miss plasma bolts being purple. This offset them nicely from the other beam and laser attacks. The contrast between beams, lasers, and plasma bolts gave a better impression of depth and variety to a battle. Now its fairly monochromatic.

I am almost certain that the Progenitor in Diplomacy had 3 plasma cannos, one on each side and one foward facing. I cant see that the forward facing plasma cannon works anymore, but then, it could be because its much harder to tell whats plasma and what is laser. I noticed because I always thought that the progenitor fought inefficiently - while not Rebellion specific, is there anyway we could get the progenitor to turn 45 degrees to its specified target intead of 90 degrees. I want to execute the current captain since he doesnt use 2 of its 3 plasma cannons when he positions the ship facing a target at 90 degrees.